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exercises/UNIX_HPC_cheat_sheet.md

+# Bash Cheat Sheet
+
+ A cheat sheet for bash commands.
+
+
+ ## Manage and navigate directories
+
+```bash
+pwd                       # Print current directory path
+ls                        # List directories
+ls -a|--all               # List directories including hidden
+ls -l                     # List directories in long form
+ls -l -h|--human-readable # List directories in long form with human readable sizes
+cd foo                    # Go to foo sub-directory
+cd                        # Go to home directory
+cd ~                      # Go to home directory
+cd -                      # Go to last directory
+```
+
+## Manage files
+
+```bash
+cp foo.txt bar.txt                                # Copy file
+mv foo.txt bar.txt                                # Move/Rename file
+rm foo.txt                                        # Delete foo.txt
+rm *                                              # Delete all files in current directory 
+ln -s foo bar                                     # Create a link 'bar' to the file 'foo'
+mkdir foo                 # Create foo directory
+rmdir foo                 # Delete empty foo directory
+rmd -r foo                # Delete foo directory including content  
+```
+
+## Read and manipulate files
+
+```bash
+cat foo.txt            # Print all contents
+less foo.txt           # Print some contents at a time (g - go to top of file, SHIFT+g, go to bottom of file, /foo to search for 'foo')
+more foo.txt           # Print some content at a time, only moving forward in document
+head foo.txt           # Print top 10 lines of file
+tail foo.txt           # Print bottom 10 lines of file
+nano foo.txt           # Simple file editor
+vi foo.txt             # Advanced file editor 
+wc foo.txt             # List number of lines, words and characters in the file
+wc -l foo.txt          # Counts the lines
+cut -d [delimiter] -f [field] foo.txt     # Cuts out the specified fields that are separated by the specified delimiter out of each line of a file
+touch foo.txt           # Create empty file if it does not exist or change "modified by" date of existing file    
+```
+
+## Input and Output
+
+```bash
+echo "Hello world!"         # Print statement to standard output
+echo "foo" > bar.txt        # Direct output into file. Overwrites file if it already exists.
+echo "foo" >> bar.txt       # Direct output into file and append if it already exists. 
+command1 | command2         # Directs output from command1 as standard input into command2    
+```
+<br><br>
+
+
+## Variables and arrays
+
+```bash
+myvar="foobar"              # Assign string to a variable
+$myvar                      # Calling the variable
+output=$(command)           # Assign output of a command to a variable
+array=(x1 x2 x3 x4)         # Create an array 
+${array[@]}                 # Access the whole array
+${array[0]}                 # Access the 1st element
+${!array[@]}                # Get indeces of all array elements
+```
+
+## Control structures
+
+For loop:
+```bash
+for i in {1..n}             
+do
+    command $i
+done 
+```
+
+While loop:
+```bash
+while [ condition ]             
+do
+    command $i
+done 
+```
+
+If else:
+```bash
+if [ condition ]
+then
+    command1
+else
+    command2
+fi
+```
+
+
+<br>
+
+# SLURM Cheat Sheet
+
+## Connect to Science Cluster
+
+```bash
+ssh shortname@cluster.s3it.uzh.ch
+```
+
+## Copy files to Science Cluster
+
+```bash
+scp foo.txt <shortname>@cluster.s3it.uzh.ch:<target directory>
+```
+
+
+## Submitting jobs
+
+In a script `myjob.sh`:
+```bash
+#!/usr/bin/env bash
+#SBATCH --cpus-per-task=[number]
+#SBATCH --mem=[memory]
+#SBATCH --time=[hr:min:sec]
+#SBATCH --job-name=[name]
+#SBATCH --output=[name]_%j.out
+#SBATCH --error=[name]_%j.err
+
+# load any required modules 
+module load [module name]
+
+command1
+command2
+command3
+```
+Submit script as job to the computing nodes:
+```bash
+sbatch myjob.sh
+```
+
+